revised input

inputs

@@ -1,15 +1,15 @@
 {
     "{{ project_name }}.read1": "{{ read1 }}",
     "{{ project_name }}.read2": "{{ read2 }}",
-    "{{ project_name }}.idx": "{{ idx }}",
-    "{{ project_name }}.gtf": "{{ gtf }}",
-    "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
-    "{{ project_name }}.hisat2.docker": "{{ hisat2_docker }}",
-    "{{ project_name }}.hisat2.cluster": "{{ hisat2_cluster }}",
-    "{{ project_name }}.samtools.docker": "{{ samtools_docker }}",
-    "{{ project_name }}.samtools.cluster": "{{ samtools_cluster }}",
-    "{{ project_name }}.stringtie.docker": "{{ stringtie_docker }}",
-    "{{ project_name }}.stringtie.cluster": "{{ stringtie_cluster }}"
-    "{{ project_name }}.ballgown.docker": "{{ ballgown_docker }}",
-    "{{ project_name }}.ballgown.cluster": "{{ ballgown_cluster }}"
-}
+    "{{ project_name }}.idx": "{{ idx if idx != '' else 'oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/' }}",
+    "{{ project_name }}.gtf": "{{ gtf if gtf != '' else 'oss://pgx-reference-data/reference/tophat2/annotation/gencode.v22.annotation.gtf' }}",
+    "{{ project_name }}.idx_prefix": "{{ idx_prefix if idx_prefix != '' else 'genome_snp_tran' }}",
+    "{{ project_name }}.hisat2_docker": "{{ hisat2_docker if hisat2_docker != '' else 'registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2' }}",
+    "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster if hisat2_cluster != '' else 'OnDemand bcs.a2.3xlarge img-ubuntu-vpc' }}",
+    "{{ project_name }}.samtools_docker": "{{ samtools_docker if samtools_docker != '' else 'registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1' }}",
+    "{{ project_name }}.samtools_cluster": "{{ samtools_cluster if samtools_cluster != '' else 'OnDemand bcs.a2.large img-ubuntu-vpc' }}",
+    "{{ project_name }}.stringtie_docker": "{{ stringtie_docker if stringtie_docker != '' else 'registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4' }}",
+    "{{ project_name }}.stringtie_cluster": "{{ stringtie_cluster if stringtie_cluster != '' else 'OnDemand bcs.a2.large img-ubuntu-vpc' }}"
+    "{{ project_name }}.ballgown_docker": "{{ ballgown_docker if ballgown_docker != '' else 'registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1' }}",
+    "{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster if ballgown_cluster != '' else 'OnDemand bcs.a2.large img-ubuntu-vpc' }}"
+}

samples.csv

@@ -0,0 +1,2 @@
+hisat2_cluster,samtools_cluster,stringtie_docker,ballgown_cluster,read1,idx_prefix,ballgown_docker,idx,gtf,sample_id,hisat2_docker,stringtie_cluster,samtools_docker,read2
+,,,,oss://pgx-result/shangjun/test_data/test_R1.fq.gz,,,,,test,,,,oss://pgx-result/shangjun/test_data/test_R2.fq.gz

workflow.wdl

@@ -13,19 +13,35 @@ workflow {{ project_name }} {
 	
 	
 	call hisat2.hisat2 as hisat2 {
-		input: idx=idx, idx_prefix=idx_prefix, read_1P=read1, read_2P=read2
+		input: 
+		docker = hisat2_docker,
+		cluster = hisat2_cluster,
+		idx=idx, 
+		idx_prefix=idx_prefix, 
+		read_1P=read1, 
+		read_2P=read2
 	}
 
     all samtools.samtools as samtools {
-        input: sam = hisat2.sam
+        input: 
+		docker = samtools_docker,
+		cluster = samtools_cluster,
+		sam = hisat2.sam
 	}
 
     call stringtie.stringtie as stringtie {
-        input: gtf = gtf, bam = samtools.out_bam
+        input: 
+		docker = stringtie_docker,
+		cluster = stringtie_cluster,
+		gtf = gtf, 
+		bam = samtools.out_bam
 	}   
 
 	call ballgown.ballgown as ballgown {
-		input: ballgown = stringtie.ballgown
+		input: 
+		docker = ballgown_docker,
+		cluster = ballgown_cluster,
+		ballgown = stringtie.ballgown
 	}